1 Pre-work

Prior to the workshop, we recommend you start by:

  • Having the latest version of R installed (at least 4.3)

  • Having the latest version of RStudio installed

  • Installing the STexampleData, imcdatasets, scHOT, spicyR, simpleSeg and lisaClust packages Bioconductor and associated dependencies

If you use use RStudio, we recommend viewing this document in visual mode.

1.1 Installing required R packages

The following chunk of code will install all of the R packages you need for this workshop. Please ensure that you do not run it more than once or remove eval=FALSE from the code chunk, you do not want to be installing these packages multiple times.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("STexampleData", "imcdatasets", "scHOT", "simpleSeg", "FuseSOM", "spicyR", "lisaClust", "ClassifyR", "ggplot2", "scater", "scuttle", "batchelor", "patchwork", "plotly", "RColorBrewer"))

If you are viewing this Rmd before the workshop, you might also like to download the data that we will use. This can take time.

imc <- imcdatasets::Damond_2019_Pancreas(data_type = "spe")
spe <- STexampleData::seqFISH_mouseEmbryo()

2 Loading R packages and setting parameters

suppressPackageStartupMessages({
  # Data packages
  library(STexampleData)
  library(imcdatasets)
  
  # Packages from scdney
  library(scHOT)
  library(simpleSeg)
  library(FuseSOM)
  library(spicyR)
  library(lisaClust)
  library(ClassifyR)
  
  # Extra packages needed for workshop
  library(ggplot2)
  library(scater)
  library(scuttle)
  library(batchelor)
  library(patchwork)
  library(plotly)
  library(RColorBrewer)
})

# We can use the following to increase computational speed.
# If you feel confident in the amount of CPU cores and/or memory that you have 
# access to, feel free to increase nCores.

nCores <- 1 
BPPARAM <- simpleSeg:::generateBPParam(nCores)

# The following will improve the aesthetics of some of the plots that we will
# generate.
theme_set(theme_classic())
source("data/celltype_colours.R")

3 Introduction

This is the main working document for the Unlocking single cell spatial omics analyses with scdney workshop. We recommend you download a local copy of the Rmd file and while running through the analysis scripts see what edits or additions you would make.

We will use two motivating datasets:

  • Lohoff et al, 2022: A seqFISH study of early mouse organogenesis. We will use a subset of data that is made available from the STExampleData package.

  • (Damond et al, 2019): An Imaging Mass Cytometry (IMC) dataset profiling the spatial landscape of pancreatic islets in subjects with long-duration diabetes, recent onset diabetes and controls. The data is downloaded using the imcdatasets package. The key conclusion of this manuscript (amongst others) is that spatial organisation of cells is indicative of diabetes progress. We will examine this data and assess a similar question using the packages in scdney.

4 Part 1: Data structures and exploratory data analysis

Here we will download the datasets, examine the structure and perform some exploratory analyses. This might take a few moments and you may be prompted to install some additional packages.

4.1 1.1: seqFISH

Here we download the seqFISH mouse embryo data. This is a SpatialExperiment object, which extends the SingleCellExperiment object.

spe <- STexampleData::seqFISH_mouseEmbryo()
spe
## class: SpatialExperiment 
## dim: 351 11026 
## metadata(0):
## assays(2): counts molecules
## rownames(351): Abcc4 Acp5 ... Zfp57 Zic3
## rowData names(1): gene_name
## colnames(11026): embryo1_Pos0_cell10_z2 embryo1_Pos0_cell100_z2 ...
##   embryo1_Pos28_cell97_z2 embryo1_Pos28_cell98_z2
## colData names(14): cell_id embryo ... segmentation_vertices sample_id
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## spatialCoords names(2) : x y
## imgData names(0):

We can use functions designed for SingleCellExperiment objects in the scater package for plotting via the reducedDim slot. We multiply the spatial coordinates by a matrix to flip the y-axis and ensure we fix the aspect ratio.

spe <- logNormCounts(spe)
coord_transform <- matrix(c(1,0,0,-1), 2, 2, byrow = TRUE)
reducedDim(spe, "spatialCoords") <- spatialCoords(spe) %*% coord_transform
plotReducedDim(spe, "spatialCoords", colour_by = c("Sox2"), point_size = 1) +
  coord_fixed()

Questions

  1. How many cells are in this data?
  2. How many genes?
  3. Plot gene expression mapping point size to the cell area.
# try to answer the above question using the spe object. 
# you may want to check the SingleCellExperiment vignette.
# https://bioconductor.org/packages/3.17/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html

We can perform a typical gene-expression based analysis for this data. Later in part two we will perform some specific analytical techniques, but for now let’s explore the dataset and use methods designed for single cell data.

Dimensionality reduction using PCA, batch correction across tiles using the batchelor package, followed by UMAP and plotting.

spe <- runPCA(spe)

b.out <- batchelor::batchCorrect(spe, batch = spe$pos, assay.type = "logcounts", PARAM=FastMnnParam(d=20))
reducedDim(spe, "FastMnn") <- reducedDim(b.out, "corrected")
spe <- runUMAP(spe, dimred = "FastMnn")
spe
## class: SpatialExperiment 
## dim: 351 11026 
## metadata(0):
## assays(3): counts molecules logcounts
## rownames(351): Abcc4 Acp5 ... Zfp57 Zic3
## rowData names(1): gene_name
## colnames(11026): embryo1_Pos0_cell10_z2 embryo1_Pos0_cell100_z2 ...
##   embryo1_Pos28_cell97_z2 embryo1_Pos28_cell98_z2
## colData names(15): cell_id embryo ... sample_id sizeFactor
## reducedDimNames(4): spatialCoords PCA FastMnn UMAP
## mainExpName: NULL
## altExpNames(0):
## spatialCoords names(2) : x y
## imgData names(1): sample_id
g_celltype_umap <- plotReducedDim(spe, "UMAP", colour_by = "celltype_mapped_refined") + 
  scale_colour_manual(values = celltype_colours)
g_celltype_umap

plotReducedDim(spe, "UMAP", colour_by = "Sox2")

g_celltype_spatial <- plotReducedDim(spe, "spatialCoords", colour_by = "celltype_mapped_refined") + 
  scale_colour_manual(values = celltype_colours) + 
  coord_fixed()

g_all <- g_celltype_spatial + theme(legend.position = "none") + g_celltype_umap
g_all

Advanced/Extension Question

  1. What considerations need to be made for batch correction of spatial data? What assumptions are being made and/or broken? How could you check this?
  2. Check out the ggiraph package for extending the g_all object to an interactive plot with a tooltip that links the spatial and UMAP coordinate systems. (Hint: This may involve generating a new ggplot object outside of the plotReducedDim function.)
# try to examine answer the above questions using the spe object. 
# you may want to set up some small simulation..

At this point we will pause our examination of the seqFISH dataset that is in the object spe, and turn over to the second example dataset. In the second part we will revisit this data for performing scHOT testing.

4.2 1.2: IMC

Here we download a subset of the IMC data from the imcdatasets package. This is also a SpatialExperiment object.

imc <- imcdatasets::Damond_2019_Pancreas(data_type = "spe")
imc
## class: SpatialExperiment 
## dim: 38 252059 
## metadata(0):
## assays(3): counts exprs quant_norm
## rownames(38): H3 SMA ... DNA1 DNA2
## rowData names(6): channel metal ... antibody_clone full_name
## colnames(252059): 138_1 138_2 ... 319_1149 319_1150
## colData names(27): cell_id image_name ... patient_BMI sample_id
## reducedDimNames(0):
## mainExpName: Damond_2019_Pancreas_v1
## altExpNames(0):
## spatialCoords names(2) : cell_x cell_y
## imgData names(0):

Questions

  1. How many cells are in this data?
  2. How many markers? How many images?
  3. Are there any interesting patient characteristics?
# try to answer the above question using the imc object. 
# you may want to check the SingleCellExperiment vignette.
# https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html

To make things faster and less computationally demanding, we’ll subset the data down to 60 pancreatic islets from an equal number of non-diabetic, recent onset and long-duration diabetics.

# set the seed so the sampling is determined
set.seed(51773)

# sample 20 image names from the 3 conditions
useImages <- c(
  sample(imc$image_name[imc$patient_stage == "Non-diabetic"], 20),
  sample(imc$image_name[imc$patient_stage == "Onset"], 20),
  sample(imc$image_name[imc$patient_stage == "Long-duration"], 20)
)

# subset the data with the images names we sampled
imc <- imc[, imc$image_name %in% useImages]

As our data is stored in a SpatialExperiment, as we did previously, we can use scater to perform and visualise our data in a lower dimensional embedding to look for image or cluster differences.

set.seed(51773)
# Perform dimension reduction using UMAP.
imc <- scater::runUMAP(imc, exprs_values = "counts", name = "UMAP_raw")

# UMAP by imageID.
scater::plotReducedDim(imc, dimred = "UMAP_raw", colour_by = "image_name")

Questions

  1. Is this UMAP highlighting any “interesting” structure in the data?
  2. What does it mean that cells from different images cluster together? Can you modify this to look for relationships to disease stage?
  3. One of the columns contains the cell types defined by Damond et al., are these cell types separated on the UMAP?
# try to answer the questions here!

We should check to see if the marker intensities of each cell require some form of transformation or normalisation to control for subtle systematic differences that may have emerged during measurement.

Here, we extract the intensities from the counts assay. Looking at SMA, which should be expressed in the majority of the stromal cells, we can see that the intensities are clearly very skewed and the peaks of the lower intensities don’t overlap.

# Extract marker data and bind with information about images
df <- as.data.frame(cbind(colData(imc), t(assay(imc, "counts"))))

# Plots densities of PanKRT for each image.
ggplot(df, aes(x = sqrt(SMA), colour = image_name)) +
  geom_density() +
  theme(legend.position = "none") +
  xlim(0,4) +
  labs(x = "SMA", y = "Density by Image")

We can transform and normalise our data using the normalizeCells function. Here we have taken the intensities from the counts assay, performed an inverse hyperbolic sine transform, then for each image trimmed the 99 quantile, scaled the means to be equal and then removed the first principal component. This modified data is then store in the norm assay by default. We can see that this normalised data appears to align more, not perfect, but likely sufficient for clustering.

# Transform and normalise the marker expression of each cell type.
# Use a square root transform, then trimmed the 99 quantile
imc <- simpleSeg::normalizeCells(imc,
  transformation = "asinh",
  method = c("trim99", "mean", "PC1"),
  assayIn = "counts",
  cores = nCores,
  imageID = "image_name"
)

# Extract normalised marker information.
df <- as.data.frame(cbind(colData(imc), t(assay(imc, "norm"))))

# Plots densities of normalised PanKRT for each image.
ggplot(df, aes(x = SMA, colour = image_name)) +
  geom_density() +
  theme(legend.position = "none")

Questions

  1. Do different normalisation methods (e.g., ‘mean’, ‘minMax’, ‘trim99’, ‘PC1’) or transforms (sqrt) look different?
  2. What about different markers?
# try to answer the questions here!

At this point you should have a sense of the data structure and feel confident in generating visualisations and finding information on how to perform other kinds of explorations. Time for a few minutes to stand up and stretch and get ready for Part 2.

5 Part 2: Analytical techniques

Now that are we are comfortable with the two datasets, let’s perform some analytical techniques that are specific to spatial omics data.

5.1 scHOT analysis of the developing brain

Here we will ask which gene patterns we observe to be changing across the spe$gutRegion cell type in space. Note that we want to assess the anatomical region corresponding to the anterior end of the developing gut developing brain so we will first subset the cells using the spatial coordinates. We can check what we have selected by plotting.

spe$gutRegion <- spe$celltype_mapped_refined == "Gut tube" &
  reducedDim(spe, "spatialCoords")[,1] < -0.5

plotReducedDim(spe, "spatialCoords", colour_by = "gutRegion") + 
  coord_fixed() + 
  scale_colour_manual(values = c("TRUE" = "red", "FALSE" = "grey"))

Let’s subset the data to only these cells and continue with our scHOT analysis.

spe_gut <- spe[,spe$gutRegion]
spe_gut
## class: SpatialExperiment 
## dim: 351 472 
## metadata(0):
## assays(3): counts molecules logcounts
## rownames(351): Abcc4 Acp5 ... Zfp57 Zic3
## rowData names(1): gene_name
## colnames(472): embryo1_Pos3_cell377_z2 embryo1_Pos3_cell388_z2 ...
##   embryo1_Pos27_cell74_z2 embryo1_Pos28_cell373_z2
## colData names(16): cell_id embryo ... sizeFactor gutRegion
## reducedDimNames(4): spatialCoords PCA FastMnn UMAP
## mainExpName: NULL
## altExpNames(0):
## spatialCoords names(2) : x y
## imgData names(1): sample_id

We select genes with at least some proportion of expressed cells for testing, and create the scHOT object.

hist(rowMeans(counts(spe_gut)>0), 40)

gene_to_test <- as.matrix(c(rownames(spe_gut[rowMeans(counts(spe_gut)>0) > 0.2,])))
length(gene_to_test)
## [1] 165
rownames(gene_to_test) <- apply(gene_to_test, 1, paste0, collapse = "_")
head(gene_to_test)
##         [,1]     
## Acvr1   "Acvr1"  
## Acvr2a  "Acvr2a" 
## Ahnak   "Ahnak"  
## Akr1c19 "Akr1c19"
## Aldh1a2 "Aldh1a2"
## Aldh2   "Aldh2"
scHOT_spatial <- scHOT_buildFromSCE(spe_gut,
                                    assayName = "logcounts",
                                    positionType = "spatial",
                                    positionColData = c("x_global_affine", "y_global_affine"))

scHOT_spatial
## class: scHOT 
## dim: 351 472 
## metadata(0):
## assays(1): expression
## rownames(351): Abcc4 Acp5 ... Zfp57 Zic3
## rowData names(0):
## colnames(472): embryo1_Pos3_cell377_z2 embryo1_Pos3_cell388_z2 ...
##   embryo1_Pos27_cell74_z2 embryo1_Pos28_cell373_z2
## colData names(16): cell_id embryo ... sizeFactor gutRegion
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## testingScaffold dim: 0 0 
## weightMatrix dim: 0 0 
## scHOT_output colnames (0):
## param names (0):
## position type: spatial

We now add the testing scaffold to the scHOT object, and set the local weight matrix for testing, with a choice of span of 0.1 (the proportion of cells to weight around each cell). We can speed up computation by not requiring the weight matrix correspond to every individual cell, but instead a random selection among all the cells using the thin function.

scHOT_spatial <- scHOT_addTestingScaffold(scHOT_spatial, gene_to_test)
head(scHOT_spatial@testingScaffold)
##         gene_1   
## Acvr1   "Acvr1"  
## Acvr2a  "Acvr2a" 
## Ahnak   "Ahnak"  
## Akr1c19 "Akr1c19"
## Aldh1a2 "Aldh1a2"
## Aldh2   "Aldh2"
scHOT_spatial <- scHOT_setWeightMatrix(scHOT_spatial, span = 0.2)
scHOT_spatial@weightMatrix <- thin(scHOT_spatial@weightMatrix, n = 50)

dim(slot(scHOT_spatial, "weightMatrix"))
## [1]  53 472

For a given cell we can visually examine the local weight given by the span parameter.

cellID = 10

df <- cbind(as.data.frame(colData(scHOT_spatial)),
      W = slot(scHOT_spatial, "weightMatrix")[cellID,])

ggplot(df,
       aes(x = x_global_affine, y = -y_global_affine)) +
  geom_point(aes(colour = W, size = W)) +
  scale_colour_gradient(low = "black", high = "purple") +
  scale_size_continuous(range = c(0.5,2.5)) +
  theme_classic() +
  guides(colour = guide_legend(title = "Spatial Weight"),
         size = guide_legend(title = "Spatial Weight")) +
  ggtitle(paste0("Central cell: ", cellID)) + 
  coord_fixed() +
  NULL

Question

  1. How will the results change if the span is increased/decreased?
## Make associated changes to the code to test out the question above.

We set the higher order function as the weighted mean function, and then calculate the observed higher order test statistics. This may take around 10 seconds.

scHOT_spatial <- scHOT_calculateGlobalHigherOrderFunction(
    scHOT_spatial,
    higherOrderFunction = weightedMean,
    higherOrderFunctionType = "weighted")

slot(scHOT_spatial, "scHOT_output")
## DataFrame with 165 rows and 2 columns
##              gene_1 globalHigherOrderFunction
##         <character>                  <matrix>
## Acvr1         Acvr1                  0.216666
## Acvr2a       Acvr2a                  0.375776
## Ahnak         Ahnak                  0.976418
## Akr1c19     Akr1c19                  0.744070
## Aldh1a2     Aldh1a2                  0.245981
## ...             ...                       ...
## Wnt5a         Wnt5a                  0.335820
## Wnt5b         Wnt5b                  0.220300
## Xist           Xist                  1.162241
## Zfp444       Zfp444                  0.744082
## Zfp57         Zfp57                  0.595519
scHOT_spatial <- scHOT_calculateHigherOrderTestStatistics(
    scHOT_spatial, na.rm = TRUE)

Now we can plot the overall mean versus the scHOT statistic to observe any relationship. Labels can be interactively visualised using ggplotly. Some genes may have different distributions so we turn to permutation testing to assess statistical significance.

g <- ggplot(as.data.frame(scHOT_spatial@scHOT_output), 
           aes(x = globalHigherOrderFunction, y = higherOrderStatistic, label = gene_1)) + 
  xlab("Mean across all cells") +
  ylab("scHOT statistic for local weightedMean") +
  geom_point()
g

ggplotly(g)

Set up the permutation testing schema. For the purposes of this workshop we set a low number of permutations over a low number of genes in the testing scaffold, you may want to change this as you work through the workshop yourself. The testing will take a few minutes to run, here with the parallel parameters that were set at the beginning of this document.

scHOT_spatial <- scHOT_setPermutationScaffold(scHOT_spatial,
                                              numberPermutations = 50,
                                              numberScaffold = 30)

scHOT_spatial <- scHOT_performPermutationTest(
    scHOT_spatial,
    verbose = TRUE,
    parallel = FALSE)
## Permutation testing combination 40 of 165...
## Permutation testing combination 50 of 165...
## Permutation testing combination 80 of 165...
## Permutation testing combination 150 of 165...
slot(scHOT_spatial, "scHOT_output")
## DataFrame with 165 rows and 9 columns
##              gene_1 globalHigherOrderFunction            higherOrderSequence
##         <character>                  <matrix>                  <NumericList>
## Acvr1         Acvr1                  0.216666 0.251205,0.275076,0.286668,...
## Acvr2a       Acvr2a                  0.375776 0.398236,0.376223,0.361763,...
## Ahnak         Ahnak                  0.976418    1.23931,1.22101,1.19278,...
## Akr1c19     Akr1c19                  0.744070 0.681732,0.622183,0.625407,...
## Aldh1a2     Aldh1a2                  0.245981 0.117491,0.118105,0.121221,...
## ...             ...                       ...                            ...
## Wnt5a         Wnt5a                  0.335820 0.282418,0.280240,0.268180,...
## Wnt5b         Wnt5b                  0.220300 0.262440,0.321449,0.368172,...
## Xist           Xist                  1.162241    1.18893,1.17123,1.18238,...
## Zfp444       Zfp444                  0.744082 0.529888,0.531771,0.538540,...
## Zfp57         Zfp57                  0.595519 0.853046,0.844188,0.838651,...
##         higherOrderStatistic numberPermutations storePermutations
##                    <numeric>          <numeric>         <logical>
## Acvr1              0.0750954                  0              TRUE
## Acvr2a             0.0665143                  0              TRUE
## Ahnak              0.3319897                  0              TRUE
## Akr1c19            0.1673342                  0              TRUE
## Aldh1a2            0.1827836                  0              TRUE
## ...                      ...                ...               ...
## Wnt5a               0.172300                  0              TRUE
## Wnt5b               0.104924                  0              TRUE
## Xist                0.120828                  0              TRUE
## Zfp444              0.118930                 50              TRUE
## Zfp57               0.130128                  0              TRUE
##                              permutations pvalPermutations FDRPermutations
##                             <NumericList>        <numeric>       <numeric>
## Acvr1                                  NA               NA              NA
## Acvr2a                                 NA               NA              NA
## Ahnak                                  NA               NA              NA
## Akr1c19                                NA               NA              NA
## Aldh1a2                                NA               NA              NA
## ...                                   ...              ...             ...
## Wnt5a                                  NA               NA              NA
## Wnt5b                                  NA               NA              NA
## Xist                                   NA               NA              NA
## Zfp444  0.0582096,0.0537059,0.0641674,...             0.04           0.044
## Zfp57                                  NA               NA              NA

After the permutation test we can estimate the P-values across all genes.

scHOT_plotPermutationDistributions(scHOT_spatial)

scHOT_spatial <- scHOT_estimatePvalues(scHOT_spatial,
                                       nperm_estimate = 100,
                                       maxDist = 0.1)
slot(scHOT_spatial, "scHOT_output")
## DataFrame with 165 rows and 14 columns
##              gene_1 globalHigherOrderFunction            higherOrderSequence
##         <character>                  <matrix>                  <NumericList>
## Acvr1         Acvr1                  0.216666 0.251205,0.275076,0.286668,...
## Acvr2a       Acvr2a                  0.375776 0.398236,0.376223,0.361763,...
## Ahnak         Ahnak                  0.976418    1.23931,1.22101,1.19278,...
## Akr1c19     Akr1c19                  0.744070 0.681732,0.622183,0.625407,...
## Aldh1a2     Aldh1a2                  0.245981 0.117491,0.118105,0.121221,...
## ...             ...                       ...                            ...
## Wnt5a         Wnt5a                  0.335820 0.282418,0.280240,0.268180,...
## Wnt5b         Wnt5b                  0.220300 0.262440,0.321449,0.368172,...
## Xist           Xist                  1.162241    1.18893,1.17123,1.18238,...
## Zfp444       Zfp444                  0.744082 0.529888,0.531771,0.538540,...
## Zfp57         Zfp57                  0.595519 0.853046,0.844188,0.838651,...
##         higherOrderStatistic numberPermutations storePermutations
##                    <numeric>          <numeric>         <logical>
## Acvr1              0.0750954                  0              TRUE
## Acvr2a             0.0665143                  0              TRUE
## Ahnak              0.3319897                  0              TRUE
## Akr1c19            0.1673342                  0              TRUE
## Aldh1a2            0.1827836                  0              TRUE
## ...                      ...                ...               ...
## Wnt5a               0.172300                  0              TRUE
## Wnt5b               0.104924                  0              TRUE
## Xist                0.120828                  0              TRUE
## Zfp444              0.118930                 50              TRUE
## Zfp57               0.130128                  0              TRUE
##                              permutations pvalPermutations FDRPermutations
##                             <NumericList>        <numeric>       <numeric>
## Acvr1                                  NA               NA              NA
## Acvr2a                                 NA               NA              NA
## Ahnak                                  NA               NA              NA
## Akr1c19                                NA               NA              NA
## Aldh1a2                                NA               NA              NA
## ...                                   ...              ...             ...
## Wnt5a                                  NA               NA              NA
## Wnt5b                                  NA               NA              NA
## Xist                                   NA               NA              NA
## Zfp444  0.0582096,0.0537059,0.0641674,...             0.04           0.044
## Zfp57                                  NA               NA              NA
##         numberPermutationsEstimated globalLowerRangeEstimated
##                           <integer>                 <numeric>
## Acvr1                            50                  0.270287
## Acvr2a                           50                  0.412098
## Ahnak                          1100                  0.270287
## Akr1c19                         100                  0.744082
## Aldh1a2                          50                  0.270287
## ...                             ...                       ...
## Wnt5a                           100                  0.270287
## Wnt5b                            50                  0.270287
## Xist                            100                  1.163058
## Zfp444                          100                  0.744082
## Zfp57                           100                  0.508846
##         globalUpperRangeEstimated pvalEstimated FDREstimated
##                         <numeric>     <numeric>    <numeric>
## Acvr1                    0.270287   0.100000000    0.1231343
## Acvr2a                   0.412098   0.480000000    0.5109677
## Ahnak                    3.171420   0.000908265    0.0239130
## Akr1c19                  0.809843   0.009900990    0.0239130
## Aldh1a2                  0.270287   0.019607843    0.0282051
## ...                           ...           ...          ...
## Wnt5a                    0.412098    0.00990099    0.0239130
## Wnt5b                    0.270287    0.01960784    0.0282051
## Xist                     1.230984    0.26000000    0.2958621
## Zfp444                   0.809843    0.04000000    0.0532258
## Zfp57                    0.611378    0.03000000    0.0415966

We can now examine the spatial expression of the 5 most significant genes, both in our scHOT object and over our original spe object.

output_sorted <- slot(scHOT_spatial, "scHOT_output")[order(slot(scHOT_spatial,
                                                                "scHOT_output")$pvalEstimated),]
topgenes <- rownames(output_sorted)[1:5]

reducedDim(scHOT_spatial, "spatialCoords") <- reducedDim(spe, "spatialCoords")[colnames(scHOT_spatial),]

for (topgene in topgenes) {
  g_spe <- plotReducedDim(spe, "spatialCoords", colour_by = c(topgene), point_size = 1) +
    coord_fixed()
  
  g_scHOT <- plotReducedDim(scHOT_spatial, "spatialCoords", colour_by = c(topgene), point_size = 1,
                           by_exprs_values = "expression") +
    coord_fixed()
  
  g_all <- g_scHOT + g_spe
  print(g_all)
}

Here we are noting the genes that are found to have the most statistically significant spatial variation in their local mean expression. These genes point to specific patterns that govern the development of individual parts of the gut tube.

Advanced/Extended Questions

  1. How would you perform such testing over multiple distinct samples?
  2. scHOT is developed with all higher order testing in mind, use the associated vignette to get towards assessing changes in variation or correlation structure in space.
## try some code

Now that we have assessed genes varying in expression in space, let’s look further into the IMC data where we will make use of the multiple samples to perform clustering and extract some biological understanding.

5.2 A very spicy analysis of the IMC data

First, let’s select the markers that we’d like to use to cluster the cells. Clustering partitions the data by the largest sources of variation. If there are lots of markers for a specific cell type, this will cluster very well.

This step requires domain knowledge about how different cells express different markers. Using irrelevant markers to cluster the cells will lead to meaningless clusters.

useMarkers <- c(
  "NKX6_1", #   Homeobox protein Nkx-6.1    β   169Tm
  "IAPP", #     Amylin  β   167Er
  "GCG", #  Glucagon    α   156Gd
  "PCSK2", # Proprotein convertase 2    α   144Nd
  "SST", # Somatostatin δ   159Tb
  "PPY", # Pancreatic polypeptide   γ   153Eu
  "PDX1", # Pancreatic and duodenal homeobox 1  β, δ, ductal    158Gd
  "SYP", # Synaptophysin    Endocrine   160Gd
  "CD99", # CD99    Endocrine   145Nd
  "SLC2A1", # Glucose transporter 1 Endocrine   148Nd
  "PTPRN", # Receptor-type tyrosine-protein phosphatase-like N  Endocrine   174Yb
  "AMY2A", # Pancreatic amylase Acinar  150Nd
  "KRT19", # Cytokeratin 19 Ductal  161Dy
  "CD44", # CD44    Exocrine    143Nd
  "CD45", # CD45    Immune  162Dy
  "CD45RA", # CD45RA    Immune  164Dy
  "CD3e", # CD3ɛ    T   152Sm
  "CD4", # CD4  Helper T    171Yb
  "CD8a", # CD8a    Cytotoxic T 165Ho
  "CD20", # CD20    B   149Sm
  "CD68", # CD68    Monocytes, macrophages  146Nd
  "MPO", # Myeloperoxidase  Neutrophils 147Sm
  "FOXP3", # Forkhead box P3    Regulatory T    163Dy
  "CD38", # CD38    Immune  142Nd
  "CDH1", # E-/P-cadherin   Epithelial  173Yb
  "CD31", # CD31    Endothelial 172Yb
  "SMA", # Smooth muscle actin  Stromal 115In
  "Ki67", # Ki-67   Proliferating   168Er
  "p_HH3", # Phospho-histone H3 Proliferating   170Er
  "p_Rb", # Phospho-retinoblastoma  Cycling 175Yb
  "cPARP_cCASP3", # Cleaved caspase 3 + cleaved poly (ADP-ribose) polymerase    Apoptotic   176Yb
  "CA9" # Carbonic anhydrase IX Hypoxic 166Er
)

5.2.1 Identifying cell types in the data.

Clustering

Here we cluster using the runFuseSOM function. We have chosen to specify the same subset of markers used in the original manuscript for gating cell types. We have also specified the number of clusters to identify to be numClusters = 13.

set.seed(51773)

imc <- runFuseSOM(imc,
  markers = useMarkers,
  assay = "norm",
  numClusters = 13
)

Clusters Selection

We can check to see how reasonable our choice of 13 clusters is using the estimateNumCluster and the optiPlot functions. Here we examine the Gap method, others such as jump, silhouette and within cluster distance are also available.

imc <- estimateNumCluster(imc, kSeq = 2:30)
optiPlot(imc, method = "gap")

imc@metadata$clusterEstimation$Discriminant
## [1] 12

Cluster Interpretation

We can begin the process of understanding what each of these cell clusters are by using the plotGroupedHeatmap function from scater. At the least, here, we can see we capture a few different populations of islet cells and a few immune cell populates (including CD4+ Tcells and CD8+ Tcells).

scater::plotGroupedHeatmap(imc,
  features = useMarkers,
  group = "clusters",
  exprs_values = "exprs",
  center = TRUE,
  scale = TRUE,
  zlim = c(-3, 3),
  cluster_rows = FALSE,
  block = "clusters" #block is needed because of a current bug in the function.
)

Damond et al. define their cell types using a stepwise clustering procedure with manual merge of clusters. We can compare our clustering to theirs.

regionMap(imc, cellType = "clusters", region = "cell_type") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

Checking Cluster Frequencies

We find it always useful to check the number of cells in each cluster.

# Check cluster frequencies.
colData(imc)$clusters |>
  table() |>
  sort()
## 
##  cluster_6 cluster_12  cluster_4  cluster_2  cluster_3 cluster_13 cluster_10 
##        887       1400       1552       1914       1964       2207       2980 
## cluster_11  cluster_1  cluster_7  cluster_8  cluster_5  cluster_9 
##       3397       4071       4836       6279      33877      56023

Visualise cell types in an image

Look at the distribution of cells types in an image

reducedDim(imc, "spatialCoords") <- spatialCoords(imc)

plotReducedDim(imc[, imc$image_name == "E02"], "spatialCoords", colour_by = "clusters")

Questions

  1. Does changing the normalisation affect the clustering?
  2. Does changing the number of clusters?
# try to answer the questions here!

Testing Relationships

Next, we test if there is an association between the proportion of each cell type in our clusters and progression status of disease. To do this, we recommend using a package such as diffcyt for testing for changes in abundance of cell types. However, the colTest function from spicyR allows us to quickly test for associations between the proportions of the cell types and disease status using either Wilcoxon rank sum tests or t-tests. Here we see a couple of p-values less than 0.05.

# Select cells which belong to Non-diabetic individuals and those with recent onset diabetes.
cellsToUse <- imc$patient_stage %in% c("Non-diabetic", "Onset")

# Perform simple t tests on the columns of the proportion matrix.
testProp <- colTest(imc[, cellsToUse],
  condition = "patient_stage",
  feature = "clusters",
  imageID = "image_name"
)
testProp
##            mean in group Non-diabetic mean in group Onset     t    pval adjPval
## cluster_3                      0.0360             0.00100 21.00 3.3e-12 4.3e-11
## cluster_13                     0.0630             0.00024 12.00 4.7e-08 3.1e-07
## cluster_2                      0.0056             0.02600 -6.80 2.1e-06 9.1e-06
## cluster_8                      0.0390             0.07300 -5.90 8.9e-06 2.9e-05
## cluster_7                      0.0480             0.03400  6.30 1.1e-05 2.9e-05
## cluster_6                      0.0049             0.00940 -3.80 9.7e-04 2.1e-03
## cluster_11                     0.0220             0.04600 -3.10 7.6e-03 1.4e-02
## cluster_5                      0.2700             0.29000 -2.80 9.7e-03 1.6e-02
## cluster_4                      0.0083             0.01200 -2.80 1.1e-02 1.6e-02
## cluster_10                     0.0230             0.02500 -1.10 3.0e-01 3.9e-01
## cluster_12                     0.0080             0.00910 -0.78 4.5e-01 5.3e-01
## cluster_1                      0.0350             0.03500  0.13 9.0e-01 9.0e-01
## cluster_9                      0.4400             0.44000 -0.13 9.0e-01 9.0e-01
##               cluster
## cluster_3   cluster_3
## cluster_13 cluster_13
## cluster_2   cluster_2
## cluster_8   cluster_8
## cluster_7   cluster_7
## cluster_6   cluster_6
## cluster_11 cluster_11
## cluster_5   cluster_5
## cluster_4   cluster_4
## cluster_10 cluster_10
## cluster_12 cluster_12
## cluster_1   cluster_1
## cluster_9   cluster_9

5.2.2 spicyR: testing for changes in spatial relationships between cell types

Our package, spicyR, which can be found on Bioconductor, provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location. Here, we use the spicy function to test for changes in the spatial relationships between pairwise combinations of cells. We quantify spatial relationships using a combination of three radii Rs = c(20, 50, 100) and mildly account for some global tissue structure using sigma = 50.

# Select cells which belong to Non-diabetic individuals and those with recent onset diabetes.
cellsToUse <- imc$patient_stage %in% c("Non-diabetic", "Onset")

# Test for changes in pairwise spatial relationships between cell types.
spicyTest <- spicy(imc[, cellsToUse],
  condition = "patient_stage",
  cellType = "clusters",
  imageID = "image_name",
  spatialCoords = c("cell_x", "cell_y"),
  Rs = c(20, 50, 100),
  sigma = 50,
  BPPARAM = BPPARAM
)

topPairs(spicyTest, n = 10)
##                          intercept coefficient      p.value   adj.pvalue
## cluster_13__cluster_13 198.3903501 -332.421086 7.916473e-10 1.337884e-07
## cluster_7__cluster_9     1.9265714  -10.498368 1.383730e-08 8.171808e-07
## cluster_10__cluster_7  -34.3992900   38.738667 1.450617e-08 8.171808e-07
## cluster_7__cluster_10  -31.3792510   36.020947 2.939840e-08 1.085683e-06
## cluster_11__cluster_2  -88.9167734  102.045503 3.212079e-08 1.085683e-06
## cluster_2__cluster_11  -85.8936506   98.702754 6.829779e-08 1.923721e-06
## cluster_9__cluster_7     1.9090631   -8.942701 1.012202e-07 2.443745e-06
## cluster_11__cluster_7  -42.9063743   47.450995 2.407615e-07 5.086086e-06
## cluster_7__cluster_11  -39.8747474   44.537604 7.870787e-07 1.477959e-05
## cluster_6__cluster_9    -0.7721868  -19.414545 1.211581e-06 2.047572e-05
##                              from         to
## cluster_13__cluster_13 cluster_13 cluster_13
## cluster_7__cluster_9    cluster_7  cluster_9
## cluster_10__cluster_7  cluster_10  cluster_7
## cluster_7__cluster_10   cluster_7 cluster_10
## cluster_11__cluster_2  cluster_11  cluster_2
## cluster_2__cluster_11   cluster_2 cluster_11
## cluster_9__cluster_7    cluster_9  cluster_7
## cluster_11__cluster_7  cluster_11  cluster_7
## cluster_7__cluster_11   cluster_7 cluster_11
## cluster_6__cluster_9    cluster_6  cluster_9

We can visualise these tests using signifPlot.

signifPlot(spicyTest,
  breaks = c(-1.5, 3, 0.5),
  cutoff = 0.0001
)

We can view some of the interesting relationships in images. Lets first identify images with “interesting” relationships between cluster 2 (likely T cells) with cluster 11 (likely islet cells).

# Sorry, this code could be made cleaner. This seems like it would be a useful function

# Get outcome data
df <- colData(imc)[cellsToUse, c("image_name", "patient_stage")]
df <- unique(df)
rownames(df) <- df$image_name

# Extract relationship
df$spatialRelationship <- spicyTest$pairwiseAssoc[["cluster_2__cluster_11"]]

df <- as.data.frame(df)

# Visualise relationships
p1 <- ggplot(df, aes(x = patient_stage, y = spatialRelationship, label = image_name)) + 
  geom_violin() + geom_jitter()

# Use plotly to look for representative images
ggplotly(p1)

We can now plot these images using plotReducedDim.

# Lets ensure that the colours of cell types stay consistent
celltypes <- unique(imc$clusters)
cellTypeColour <- brewer.pal(length(celltypes), "Paired") |>
                    colorRampPalette()
cellTypeColour <- cellTypeColour(length(celltypes))
names(cellTypeColour) <- celltypes


# Choose which cells to highlight
imc$highlight <- imc$clusters %in% c("cluster_2", "cluster_11")
imc$islet <- imc$clusters %in% c("cluster_10", "cluster_11", "cluster_12", "cluster_13")

# Plot two images
p2 <- plotReducedDim(imc[, imc$image_name == "G17"], "spatialCoords", colour_by = "clusters", size_by = "highlight", shape_by = "islet") + scale_colour_manual(values = cellTypeColour)

p3 <- plotReducedDim(imc[, imc$image_name == "E13"], "spatialCoords", colour_by = "clusters", size_by = "highlight", shape_by = "islet") + scale_colour_manual(values = cellTypeColour)

p2+p3

Question

  1. Do the results/interpretation change if use Rs = 20 or Rs = 200
  2. Are your conclusions different if you use Damond’s cell type annotations?
# try to answer the questions here!

5.2.3 lisaClust: Describing tissue microenvrionments and cellular neighbourhoods.

Our package, lisaClust, which can be found on Bioconductor, provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalisation in multiplexed imaging data that has been segmented at a single-cell resolution. Here we use the lisaClust function to clusters cells into 5 regions with distinct spatial ordering.

set.seed(51773)

# Cluster cells into spatial regions with similar composition.
imc <- lisaClust(imc,
  k = 5,
  Rs = c(20, 50, 100),
  sigma = 50,
  spatialCoords = c("cell_x", "cell_y"),
  cellType = "clusters",
  imageID = "image_name",
  BPPARAM = BPPARAM
)

Region - cell type enrichment heatmap

We can try to interpret which spatial orderings the regions are quantifying using the regionMap function. This plots the frequency of each cell type in a region relative to what you would expect by chance.

# Visualise the enrichment of each cell type in each region
regionMap(imc, cellType = "clusters", limit = c(0.2, 5))

Visualise regions

By default, these identified regions are stored in the regions column in the colData of our object. We can quickly examine the spatial arrangement of these regions using ggplot.

plotReducedDim(imc[, imc$image_name == "E02"], "spatialCoords", colour_by = "region")

While much slower, we have also implemented a function for overlaying the region information as a hatching pattern so that the information can be viewed simultaneously with the cell type calls.

# Use hatching to visualise regions and cell types.
hatchingPlot(imc,
  imageID = "image_name",
  useImages = "E02",
  cellType = "clusters",
  spatialCoords = c("cell_x", "cell_y"),
  line.spacing = 31
) + scale_colour_manual(values = cellTypeColour)

Visualise proportions of cells from different regions

regionProp <- getProp(imc, feature = "region", imageID = "image_name")


stage <- imc |>
  colData() |>
  as.data.frame() |>
  dplyr::select("image_name", "patient_stage") |>
  unique() |>
  mutate(patient_stage = factor(patient_stage, levels = c(
    "Non-diabetic",
    "Onset",
    "Long-duration"
  )))


df <- regionProp |>
  mutate(image_name = rownames(regionProp)) |>
  dplyr::right_join(stage, by = "image_name") |>
  tidyr::pivot_longer(
    cols = starts_with("region"),
    names_to = "region",
    values_to = "proportion"
  )

ggplot(df, aes(x = region, y = proportion, colour = patient_stage)) +
  geom_boxplot()

Test for changes in proportions of the regions

# Select cells which belong to Non-diabetic individuals and those with recent onset diabetes.
cellsToUse <- imc$patient_stage %in% c("Non-diabetic", "Onset")

# Perform simple t tests on the columns of the proportion matrix.
testRegions <- colTest(imc[, cellsToUse],
  condition = "patient_stage",
  feature = "region",
  imageID = "image_name"
)

testRegions
##          mean in group Non-diabetic mean in group Onset    t    pval adjPval
## region_4                      0.120             0.00064 14.0 1.2e-08 6.0e-08
## region_1                      0.018             0.11000 -8.6 3.5e-07 8.8e-07
## region_3                      0.130             0.18000 -2.8 9.6e-03 1.6e-02
## region_2                      0.190             0.17000  1.0 3.2e-01 4.0e-01
## region_5                      0.540             0.53000  0.5 6.2e-01 6.2e-01
##           cluster
## region_4 region_4
## region_1 region_1
## region_3 region_3
## region_2 region_2
## region_5 region_5

Question

  1. Do the conclusions change using more or less regions?

5.2.4 Classifying patients with spatial features.

Our ClassifyR package, https://github.com/SydneyBioX/ClassifyR, formalises a convenient framework for evaluating classification in R. We provide functionality to easily include four key modelling stages; Data transformation, feature selection, classifier training and prediction; into a cross-validation loop. Here we use the crossValidate function to perform 5 repeats of 3-fold cross-validation (we typically use 100 repeats of 5-fold cross-validation) to evaluate the performance of an randomForest applied to three quantification of our IMC data; cell type proportions, average pairwise distances between cell-types and region proportions.

In particular, we are evaluating the effectiveness of classifying islets from people with recent onset versus long-duration diabetes.

# Create list to store data.frames
data <- list()

# Add proportions of each cell type in each image
data[["props"]] <- getProp(imc, feature = "clusters", imageID = "image_name")

# Add pairwise associations
data[["dist"]] <- getPairwise(imc,
  spatialCoords = c("cell_x", "cell_y"),
  imageID = "image_name",
  cellType = "clusters",
  Rs = c(20, 50, 100),
  sigma = 50,
  BPPARAM = BPPARAM
)


# Add proportions of each region in each image
# to the list of dataframes.
data[["regions"]] <- getProp(imc, feature = "region", imageID = "image_name")

# Get outcome data
df <- colData(imc)[, c("image_name", "patient_stage")]
df <- unique(df)
rownames(df) <- df$image_name

outcome <- df$patient_stage
names(outcome) <- df$image_name

# Only use onset vs long-duration
outcome <- outcome[outcome %in% c("Long-duration", "Onset")]
outcome <- factor(outcome)

measurements <- lapply(data, function(x) x[names(outcome), ])

# Set seed
set.seed(51773)

# Perform cross-validation of a randomForest model
# for timing reasons we select a scheme
# with 10 repeats of 3-fold cross-validation.
cv <- crossValidate(
  measurements = measurements,
  outcome = outcome,
  classifier = "randomForest",
  nFolds = 3,
  nRepeats = 5,
  nCores = nCores
)

Visualise cross-validated prediction performance

Here, we use the performancePlot function to assess the AUC from each repeat of the 3-fold cross-validation. We see that the lisaClust regions appear to capture the least amount of information that is predictive of diabetes progression status of the patients.

# Calculate AUC for each cross-validation repeat and plot.
performancePlot(cv,
  metric = "AUC",
  characteristicsList = list(x = "Assay Name")
)

Questions

  1. Could we use different classifiers?

  2. What is the balanced accuracy? Why would we select this measure instead?

# Try the code!

6 Summary

This workshop has shown how to explore some processed spatial transcriptomic and IMC datasets, as well as perform analytical techniques made available in the scdney package. We hope you enjoyed the session and will continue using some of the ideas and tools we showed you for your own research questions. Reach out to the team either directly or via the Github.

7 Version and Session Info

R version: R version 4.3.1 (2023-06-16 ucrt)
Bioconductor version: 3.17 

sessionInfo()
## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 11 x64 (build 22621)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8   
## [3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=English_Australia.utf8    
## 
## time zone: Australia/Sydney
## tzcode source: internal
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] RColorBrewer_1.1-3          BumpyMatrix_1.8.0          
##  [3] plotly_4.10.2               patchwork_1.1.2            
##  [5] batchelor_1.16.0            scater_1.28.0              
##  [7] scuttle_1.10.1              ggplot2_3.4.2              
##  [9] ClassifyR_3.4.6             survival_3.5-5             
## [11] BiocParallel_1.34.2         MultiAssayExperiment_1.26.0
## [13] generics_0.1.3              lisaClust_1.8.0            
## [15] spicyR_1.12.0               FuseSOM_1.2.0              
## [17] simpleSeg_1.2.0             scHOT_1.12.0               
## [19] imcdatasets_1.8.0           cytomapper_1.12.0          
## [21] EBImage_4.42.0              STexampleData_1.8.0        
## [23] SpatialExperiment_1.10.0    SingleCellExperiment_1.22.0
## [25] SummarizedExperiment_1.30.2 Biobase_2.60.0             
## [27] GenomicRanges_1.52.0        GenomeInfoDb_1.36.1        
## [29] IRanges_2.34.0              S4Vectors_0.38.1           
## [31] MatrixGenerics_1.12.2       matrixStats_1.0.0          
## [33] ExperimentHub_2.8.1         AnnotationHub_3.8.0        
## [35] BiocFileCache_2.8.0         dbplyr_2.3.3               
## [37] BiocGenerics_0.46.0        
## 
## loaded via a namespace (and not attached):
##   [1] spatstat.sparse_3.0-1         bitops_1.0-7                 
##   [3] httr_1.4.6                    DataVisualizations_1.3.0     
##   [5] numDeriv_2016.8-1.1           tools_4.3.1                  
##   [7] backports_1.4.1               ResidualMatrix_1.10.0        
##   [9] utf8_1.2.3                    R6_2.5.1                     
##  [11] vegan_2.6-4                   HDF5Array_1.28.1             
##  [13] lazyeval_0.2.2                mgcv_1.8-42                  
##  [15] rhdf5filters_1.12.1           permute_0.9-7                
##  [17] withr_2.5.0                   sp_2.0-0                     
##  [19] analogue_0.17-6               gridExtra_2.3                
##  [21] cli_3.6.1                     spatstat.explore_3.2-1       
##  [23] profileModel_0.6.1            labeling_0.4.2               
##  [25] sass_0.4.6                    brglm_0.7.2                  
##  [27] nnls_1.4                      spatstat.data_3.0-1          
##  [29] genefilter_1.82.1             proxy_0.4-27                 
##  [31] systemfonts_1.0.4             yulab.utils_0.0.6            
##  [33] svglite_2.1.1                 R.utils_2.12.2               
##  [35] limma_3.56.2                  rstudioapi_0.15.0            
##  [37] RSQLite_2.3.1                 gridGraphics_0.5-1           
##  [39] spatstat.random_3.1-5         car_3.1-2                    
##  [41] dplyr_1.1.2                   scam_1.2-14                  
##  [43] Matrix_1.6-0                  ggbeeswarm_0.7.2             
##  [45] fansi_1.0.4                   abind_1.4-5                  
##  [47] R.methodsS3_1.8.2             terra_1.7-39                 
##  [49] lifecycle_1.0.3               yaml_2.3.7                   
##  [51] edgeR_3.42.4                  carData_3.0-5                
##  [53] rhdf5_2.44.0                  grid_4.3.1                   
##  [55] blob_1.2.4                    promises_1.2.0.1             
##  [57] dqrng_0.3.0                   crayon_1.5.2                 
##  [59] shinydashboard_0.7.2          lattice_0.21-8               
##  [61] beachmat_2.16.0               annotate_1.78.0              
##  [63] KEGGREST_1.40.0               magick_2.7.4                 
##  [65] pillar_1.9.0                  knitr_1.43                   
##  [67] boot_1.3-28.1                 rjson_0.2.21                 
##  [69] codetools_0.2-19              glue_1.6.2                   
##  [71] FCPS_1.3.3                    data.table_1.14.8            
##  [73] vctrs_0.6.3                   png_0.1-8                    
##  [75] gtable_0.3.3                  cachem_1.0.8                 
##  [77] xfun_0.39                     princurve_2.1.6              
##  [79] S4Arrays_1.0.4                mime_0.12                    
##  [81] DropletUtils_1.20.0           coop_0.6-3                   
##  [83] pheatmap_1.0.12               interactiveDisplayBase_1.38.0
##  [85] ellipsis_0.3.2                nlme_3.1-162                 
##  [87] bit64_4.0.5                   filelock_1.0.2               
##  [89] bslib_0.5.0                   irlba_2.3.5.1                
##  [91] svgPanZoom_0.3.4              vipor_0.4.5                  
##  [93] colorspace_2.1-0              DBI_1.1.3                    
##  [95] raster_3.6-23                 mnormt_2.1.1                 
##  [97] tidyselect_1.2.0              bit_4.0.5                    
##  [99] compiler_4.3.1                curl_5.0.1                   
## [101] BiocNeighbors_1.18.0          DelayedArray_0.26.3          
## [103] scales_1.2.1                  psych_2.3.6                  
## [105] rappdirs_0.3.3                goftest_1.2-3                
## [107] tiff_0.1-11                   stringr_1.5.0                
## [109] digest_0.6.31                 minqa_1.2.5                  
## [111] fftwtools_0.9-11              spatstat.utils_3.0-3         
## [113] rmarkdown_2.23                XVector_0.40.0               
## [115] htmltools_0.5.5               pkgconfig_2.0.3              
## [117] jpeg_0.1-10                   lme4_1.1-33                  
## [119] sparseMatrixStats_1.12.0      highr_0.10                   
## [121] fastmap_1.1.1                 rlang_1.1.1                  
## [123] htmlwidgets_1.6.2             shiny_1.7.4.1                
## [125] DelayedMatrixStats_1.22.1     farver_2.1.1                 
## [127] jquerylib_0.1.4               jsonlite_1.8.5               
## [129] mclust_6.0.0                  R.oo_1.25.0                  
## [131] BiocSingular_1.16.0           RCurl_1.98-1.12              
## [133] magrittr_2.0.3                GenomeInfoDbData_1.2.10      
## [135] ggplotify_0.1.1               Rhdf5lib_1.22.0              
## [137] munsell_0.5.0                 Rcpp_1.0.10                  
## [139] viridis_0.6.3                 stringi_1.7.12               
## [141] zlibbioc_1.46.0               MASS_7.3-60                  
## [143] plyr_1.8.8                    parallel_4.3.1               
## [145] ggrepel_0.9.3                 deldir_1.0-9                 
## [147] Biostrings_2.68.1             splines_4.3.1                
## [149] tensor_1.5                    locfit_1.5-9.8               
## [151] ranger_0.15.1                 igraph_1.5.0                 
## [153] ggpubr_0.6.0                  spatstat.geom_3.2-1          
## [155] ggsignif_0.6.4                reshape2_1.4.4               
## [157] ScaledMatrix_1.8.1            XML_3.99-0.14                
## [159] BiocVersion_3.17.1            evaluate_0.21                
## [161] BiocManager_1.30.21           nloptr_2.0.3                 
## [163] tweenr_2.0.2                  httpuv_1.6.11                
## [165] tidyr_1.3.0                   purrr_1.0.1                  
## [167] polyclip_1.10-4               reshape_0.8.9                
## [169] ggforce_0.4.1                 rsvd_1.0.5                   
## [171] broom_1.0.5                   xtable_1.8-4                 
## [173] rstatix_0.7.2                 later_1.3.1                  
## [175] class_7.3-22                  viridisLite_0.4.2            
## [177] tibble_3.2.1                  lmerTest_3.1-3               
## [179] memoise_2.0.1                 beeswarm_0.4.0               
## [181] AnnotationDbi_1.62.2          cluster_2.1.4                
## [183] concaveman_1.1.0